This is not an easy problem to solve. There are two approaches to finding the leaks: one, gently pressurize the hull (with a very light pressure) and apply very lightly soaped water to the area you think there might be a leak in. The other approach, which is what I do, is to assume you have a leak (all trunks leak eventually) and to fix the leak. My approach on the Mk. 2 trunks has been three fold: First, in areas where there might be some structural damage, i.e board trailing edge slicing into the trunk, I add a layer of fiberglass with epoxy. Second, I think right above where the plastic spacers are on the bottom tends to be prone to leaking, and I fill this area with some epoxy (I used West Systems G/Flex). Finally, I apply gelocat to the entire back edge of the trunk and pull a vacuum on the hull at the same time, so this sucks into the trunk. This has worked pretty well for me. Keep in mind that you are just as likely to have a leak at the very top of the trunk as you are at the very bottom.
Also keep in mind that the front beam bolts can leak, or at least I am fairly sure they do, if you don't seal them. My boat is generally dry unless we are taking waves over the front beam.